# Parameters
sample_name = "iVIP_NRN;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_176-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_176-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"

from matlas.modisco_report import modisco_report_pipeline, display_metadata
reportfile= "/mnt/lab_data/kundaje/msharmin/mouse_hem/with_tfd/full_mouse50/filtering samples_MS2.xlsx"
sheetname = "filter23"

load data from labcluster

Using TensorFlow backend.
2019-07-23 00:11:42,362 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	vasoactive intestinal peptide-positive (VIP) inhibitory neurons
Cell Group	Neural Cells and Tissues
Experiment Name	ATAC
Experiment Group	GEO

Pipeline Output

replicate	Naïve overlap peaks	IDR peaks	TSS enrichment (< 8 is very poor <10 is low)	Final number of unique mapping, dup-filtered, chrM filtered reads	Number of reads in called peak regions	Fraction of reads in called peak regions	Number of reads in promoter regions	Fraction of reads in promoter regions	Number of reads in enhancer regions	Fraction of reads in enhancer regions
rep1	242514	180616	12.774	64095408	16560106	0.2584	8197158	0.1279	26160763	0.4083
rep2	242514	180616	13.9045	55760003	14929829	0.2678	7788042	0.1397	22925761	0.4113

Modelling Metadata

Metric	Value
auPRC	0.6056
Calibrated Recall at 50% FDR	0.257
Number of Positive Examples in Test Data	222584
Number of Negative Examples in Test Data	7848267
Imbalance Ratio in Test Data	0.0276
Test Chromosomes	chr2, chr3, chr19

from matlas.modisco_report import display_comparative_motif_sets
display_comparative_motif_sets(sample_name, homer_root, modisco_root)

TF-MoDISco is using the TensorFlow backend.

Number of CISBP motifs obtained by TF-MoDISco and Homer-denovo

Shared Motifs

Motif Name	Modisco	Homer
Rfx1
Sp3
Gabpa
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Jund		absent
Tcf3		absent
Ppara		absent
Rfx8		absent
Pbx3		absent
Creb3		absent
Tcfec		absent
Pou4f1		absent
Smarcc2		absent
Sox9		absent
Hoxc5		absent
Pou5f1		absent
Hoxc6		absent
Sox2		absent
Foxm1		absent
Nfia		absent
Mbtps2		absent
Mef2a		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Maz	absent
Dbp	absent
Sp5	absent
Atf6	absent
Zfp143	absent
Gbx1	absent
Atoh1	absent

modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_176-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_176-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_176-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 27, # seqlets: 21094, Positive for: iVIP_NRN;A;GEO

• pattern_0: # seqlets: 2552

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tcf3, Nhlh2, Tcf4, Mesp2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 2357

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfia, Nfix, Nfib, Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 2111

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 2008

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, Sp2, Sp5, Klf16, Klf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1364

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Mef2a, Mef2c, Mef2d, Mef2b

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1319

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hoxc5, Phf21a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 1311

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hoxc6, Hoxa2, Meox2, Dlx5, Dlx3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 1299

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, E2f1, Tcfap2d, Zbtb7a, Zfx

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 1023

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Jund, Fos, Fosb, Smarcc1, Junb

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 830

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rfx1, Rfx2, Arid2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 653

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sox2, Tbpl2, Pou5f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 638

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pou4f1, Pit1, Pou3f3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 631

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 582

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Gabpa, Erf, Nr2c2, Etv5, Elk1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 444

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pbx3, Foxi1, Nfya, Ybx1, Dux

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 427

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Creb3, Atf7, 9430076C15Rik, Batf3, Atf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 291

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Mbtps2, Yy1, Sp3, Wt1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 273

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tcfec, Tcfeb, Bach2, Mitf, Tcfe3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 258

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sox9, Sox4, Sox3, Sox6, Sox17

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 223

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 219

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rfx8, Rfx5, Rfx3, Rfx7, Rfx4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 55

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 55

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxm1, Sox4, Sox12, Foxd3, Sox3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 48

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 48

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pou5f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_25: # seqlets: 41

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_26: # seqlets: 34

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Ppara

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  

modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_176-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_176-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_176-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 13306, Negative for: iVIP_NRN;A;GEO

• pattern_0: # seqlets: 2413

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Snai2, Zeb1, Mesp2, Id4, Atoh8

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1988

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Yy1, Mbtps2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1653

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1196

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Zfp238, Bhlha15, Tcf21, Tcf15, Tcf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1134

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Spic, Sfpi1, Spib

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 891

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Arid3b, Hmg20b, Pit1, Onecut1, Dbx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 767

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 599

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Zbtb7b, Glis2, Glis1, Zbtb7a, Zic5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 534

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 414

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr2f6, Nr2c1, Rxra, Rarb, Ppara

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 406

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 381

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Onecut3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 186

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Smarcc1, Fos, Nfe2, Nfe2l2, Fosb

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 179

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1, Zfp143

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 137

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Klf1, Klf2, Klf3, Klf4, Klf8

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 114

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2, Esrrb, Nr6a1, Nr5a1, Prdm4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 84

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 80

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Arid3b, Dbx1, Tlx2, Onecut3, Onecut1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 71

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 42

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Arid3b, Dbx1, Tlx2, Phf21a, Lhx3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 37

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores